feat: kubernetes node resource queries

nextflow/Dockerfile.dev

@@ -4,60 +4,34 @@ WORKDIR /opt/nextflow
 
 COPY . /opt/nextflow
 
-RUN  chmod +x ./gradlew ./launch.sh ./nextflow || true
-    RUN ./gradlew clean assemble exportClasspath
+RUN chmod +x ./gradlew
 
-    RUN mkdir -p /opt/nextflow-runtime/lib \
-     && i=0; \
-        tr ':' '\n' < /opt/nextflow/.launch.classpath | while read -r path; do \
-          if [ -f "$path" ]; then \
-            name="$(basename "$path")"; \
-            target="/opt/nextflow-runtime/lib/$name"; \
-            runtime_path="/opt/nextflow/lib/$name"; \
-            if [ -e "$target" ]; then \
-              i=$((i+1)); \
-              target="/opt/nextflow-runtime/lib/${i}-$name"; \
-              runtime_path="/opt/nextflow/lib/${i}-$name"; \
-            fi; \
-            cp "$path" "$target"; \
-            echo "$runtime_path" >> /opt/nextflow-runtime/.launch.classpath.lines; \
-          fi; \
-        done \
-     && paste -sd ':' /opt/nextflow-runtime/.launch.classpath.lines > /opt/nextflow-runtime/.launch.classpath
+RUN ./gradlew clean assemble pack
 
-    RUN mkdir -p /opt/nextflow-runtime/plugins \
-     && cp /opt/nextflow/launch.sh /opt/nextflow-runtime/launch.sh \
-     && cp /opt/nextflow/nextflow /opt/nextflow-runtime/nextflow \
-     && cp -a /opt/nextflow/plugins/nf-k8s /opt/nextflow-runtime/plugins/nf-k8s
+RUN mkdir -p /tmp/nf-unpack /opt/nf-dist \
+ && cd /tmp/nf-unpack \
+ && jar xf /opt/nextflow/modules/nextflow/build/distributions/nextflow-26.04.0.zip \
+ && cp -a nextflow-*/* /opt/nf-dist/ \
+ && chmod +x /opt/nf-dist/bin/nextflow
 
+RUN mkdir -p /tmp/nxf-home/plugins/nf-k8s-1.5.2 \
+ && cd /tmp/nxf-home/plugins/nf-k8s-1.5.2 \
+ && jar xf /opt/nextflow/plugins/nf-k8s/build/distributions/nf-k8s-1.5.2.zip
+
+RUN mkdir -p /tmp/nxf-home/plugins/nf-amazon-3.9.0 \
+ && cd /tmp/nxf-home/plugins/nf-amazon-3.9.0 \
+ && jar xf /opt/nextflow/plugins/nf-amazon/build/distributions/nf-amazon-3.9.0.zip
 
 FROM eclipse-temurin:17-jre
 
 WORKDIR /opt/nextflow
 
-COPY --from=build /opt/nextflow-runtime /opt/nextflow
+COPY --from=build /opt/nf-dist /opt/nextflow
+COPY --from=build /tmp/nxf-home /opt/nextflow/.nextflow
 
-RUN chmod +x /opt/nextflow/launch.sh \
- && cp /opt/nextflow/launch.sh /opt/nextflow/nextflow \
- && chmod +x /opt/nextflow/nextflow \
- && echo "nextflow-dvfs-dev-image 0.1" > /opt/nextflow/DEV_IMAGE_MARKER
+ENV PATH="/opt/nextflow/bin:${PATH}"
+ENV NXF_HOME="/opt/nextflow/.nextflow"
+ENV NXF_PLUGINS_DIR="/opt/nextflow/.nextflow/plugins"
+ENV JAVA_OPTS="--add-opens java.base/java.nio.file.spi=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util.concurrent=ALL-UNNAMED"
 
-
-RUN mkdir -p /opt/nextflow/conf \
- && cat > /opt/nextflow/conf/scm <<'EOF'
-providers {
-    mygitea {
-        platform = 'gitea'
-        server = 'https://gitea.kleine.eulenhexe.de'
-        endpoint = 'https://gitea.kleine.eulenhexe.de/api/v1'
-    }
-}
-EOF
-
-ENV PATH="/opt/nextflow:${PATH}"
-ENV NXF_HOME="/tmp/.nextflow"
-ENV NXF_PLUGINS_MODE="dev"
-ENV NXF_PLUGINS_DIR="/opt/nextflow/plugins"
-ENV NXF_SCM_FILE="/opt/nextflow/conf/scm"
-
-ENTRYPOINT ["/opt/nextflow/launch.sh"]
+ENTRYPOINT ["/opt/nextflow/bin/nextflow"]